Locus 4795

Sequence ID	X_DroMel_CAF1
Location	12,466,711 – 12,466,873
Length	162
Max. P	0.976606

overview

Window 5

Location	12,466,711 – 12,466,816
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	85.54
Mean single sequence MFE	-34.33
Consensus MFE	-27.42
Energy contribution	-28.28
Covariance contribution	0.87
Combinations/Pair	1.17
Mean z-score	-1.81
Structure conservation index	0.80
SVM decision value	0.09
SVM RNA-class probability	0.579325
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12466711 105 + 22224390
CCGUGUAUGUAUA-ACACGUGCCG---UGGAAACUGCGCGGAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUUC-CUA
.((.((((((...-..))))))))---..(((((((.(((....)))...)))))))........(((....)))..(((((((((....))))))))).......-... ( -36.30)
>DroSec_CAF1 5542 105 + 1
CCGUGUAUGUAUA-ACACGUGCCG---UGGAAACUGCGCGGAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAAUCGACGCGUUCGCACGCGUUGUUUUUUCC-CUA
.((.((((((...-..))))))))---..(((((((.(((....)))...)))))))........(((....)))...((((((((....))))))))........-... ( -34.30)
>DroSim_CAF1 5560 105 + 1
CCGUGUAUGUAUA-ACACGUGCCG---UGGAAACUGCGCGGAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAAUCGACGCGUUCGCACGCGUUGAUUUUUCC-CUA
.((.((((((...-..))))))))---..(((((((.(((....)))...)))))))........(((....)))(((((((((((....))))))))))).....-... ( -37.90)
>DroEre_CAF1 5582 106 + 1
CCGUGUAUGUAUA-ACACGUGCCG---UGGAAACUGCGCGGAAACGCUGCCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUCCCCCA
.((.((((((...-..))))))))---..(((((((((((....))).).)))))))........(((....)))..(((((((((....)))))))))........... ( -37.20)
>DroYak_CAF1 5582 106 + 1
CCGUGUAUGUAUA-ACACGUGUCG---UGGAAACUGCGCGGAAACGCUGCCAGUUUCAGUUUUUCGCUGUAGAGCAUUCAACGCGCUUGCACGCGUUGAUUUUUCCCCCA
.(((((.......-))))).....---..(((((((((((....))).).)))))))........(((....)))..((((((((......))))))))........... ( -34.90)
>DroAna_CAF1 8797 104 + 1
UAUUUCAUAUACAUACACGUGCAGGAAAGGAAACUGCGCGA---GUUUUCCAGU-UCAGUU-UUCGGUGCCGAGCGUUCGACGCGUUCACACGCGUUUCUCCCCCC-CAA
................((((...((...((((((((.((..---........))-.)))))-)))....))..))))..(((((((....))))))).........-... ( -25.40)
>consensus
CCGUGUAUGUAUA_ACACGUGCCG___UGGAAACUGCGCGGAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUCC_CUA
.((.((((((......)))))))).....(((((((.(((....)))...)))))))........(((....)))..((((((((......))))))))........... (-27.42 = -28.28 +   0.87)

alignment

secondary structure

dotplot

Window 6

Location	12,466,747 – 12,466,846
Length	99
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	92.81
Mean single sequence MFE	-21.54
Consensus MFE	-20.76
Energy contribution	-20.48
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-1.31
Structure conservation index	0.96
SVM decision value	1.10
SVM RNA-class probability	0.915398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12466747 99 + 22224390
GAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUUC-CUAAAUCC-UAAAAAAGAACCCACAACCAUUAAG
(((((.......))))).((((((.(((....)))..(((((((((....))))))))).......-........-.....)))))).............. ( -21.70)
>DroSec_CAF1 5578 99 + 1
GAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAAUCGACGCGUUCGCACGCGUUGUUUUUUCC-CUAAAUCC-UAAAAAAGAACCCACAACCAAUAAG
(((((.......))))).((((((.(((....)))...((((((((....))))))))........-........-.....)))))).............. ( -19.70)
>DroSim_CAF1 5596 99 + 1
GAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAAUCGACGCGUUCGCACGCGUUGAUUUUUCC-CUAAAUCC-UAAAAAAGAACCCACAACCAAUAAG
(((((.......))))).((((((.(((....)))(((((((((((....))))))))))).....-........-.....)))))).............. ( -23.30)
>DroEre_CAF1 5618 101 + 1
GAAACGCUGCCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUCCCCCAAAUUCUUAAAAGAGAACCCACAAACAUUAAG
((((.((((.......)))).))))(((....)))..(((((((((....))))))))).............(((((....)))))............... ( -22.50)
>DroYak_CAF1 5618 100 + 1
GAAACGCUGCCAGUUUCAGUUUUUCGCUGUAGAGCAUUCAACGCGCUUGCACGCGUUGAUUUUUCCCCCAAAUCC-UAAAAAAGAAUCCACAAACAAUAAG
(((((.......))))).((..((((((....)))..((((((((......))))))))................-.......)))...)).......... ( -20.50)
>consensus
GAAACGCUACCAGUUUCAGUUUUUCGCUGUAGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUCC_CUAAAUCC_UAAAAAAGAACCCACAACCAAUAAG
(((((.......))))).((((((.(((....)))..((((((((......))))))))......................)))))).............. (-20.76 = -20.48 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	12,466,777 – 12,466,873
Length	96
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	92.40
Mean single sequence MFE	-14.71
Consensus MFE	-13.38
Energy contribution	-13.75
Covariance contribution	0.37
Combinations/Pair	1.15
Mean z-score	-2.26
Structure conservation index	0.91
SVM decision value	1.77
SVM RNA-class probability	0.976606
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12466777 96 + 22224390
AGAGCAUUCGACGCGUUCGCACGCGUUGAUUUUUUC-CUAAAUCCUAAAAAAGAACCCACAACCAUUAAGCCAAAAUCUAUAAAAAAAAAUUGCAAA
...(((.(((((((((....)))))))))((((((.-.((.....))..))))))....................................)))... ( -14.50)
>DroSec_CAF1 5608 96 + 1
AGAGCAAUCGACGCGUUCGCACGCGUUGUUUUUUCC-CUAAAUCCUAAAAAAGAACCCACAACCAAUAAGCCAAAAUCUAUAAAAAAAAAUUGCAAA
...(((((.(((((((....)))))))(((((((..-............))))))).................................)))))... ( -14.54)
>DroSim_CAF1 5626 95 + 1
AGAGCAAUCGACGCGUUCGCACGCGUUGAUUUUUCC-CUAAAUCCUAAAAAAGAACCCACAACCAAUAAGCCAAAAUCUAUAAAA-AAAUUUGCAAA
.(((.(((((((((((....))))))))))).))).-................................................-........... ( -16.50)
>DroYak_CAF1 5648 97 + 1
AGAGCAUUCAACGCGCUUGCACGCGUUGAUUUUUCCCCCAAAUCCUAAAAAAGAAUCCACAAACAAUAAGCCAAAAUCUAUAUAAAAAAUUUGCAAA
...(((.((((((((......))))))))...............((.....))......................................)))... ( -13.30)
>consensus
AGAGCAAUCGACGCGUUCGCACGCGUUGAUUUUUCC_CUAAAUCCUAAAAAAGAACCCACAACCAAUAAGCCAAAAUCUAUAAAAAAAAAUUGCAAA
.(((.((((((((((......)))))))))).))).............................................................. (-13.38 = -13.75 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:19 2006